Bakoš made his first football steps in his hometown club ŠK Nová Baňa. When he was 15 he moved to Nitra where he made his debut at senior level. After 5 seasons in Nitra he was transferred to Matador Púchov in July 2003. In his first season for Púchov he scored 9 goals and 8 goals in the next season. In January 2006, he signed for the Russian Premier League club Shinnik. He played only 2 matches in his first Shinnik season. The club ended last in the 2006 season and was relegated to the First Division. There he scored 3 goals in 20 matches and then came back on Slovakia, signing for Ružomberok in July 2007. He scored 16 goals for two seasons in Ružomberok. Czech manager Pavel Vrba brought Bakoš to Viktoria Plzeň in June 2009. He knew him from Púchov. Bakoš scored his first goal for Plzeň in his second match against Slovan Liberec. In 2010–11, he helped win the first Czech title ever for Plzeň, scoring 9 goals. He scored 6 goals in 5 qualifying matches for the 2011–12 UEFA Champions League. On 13 September 2011, Bakoš scored the first UEFA Champions League group stage goal in Viktoria Plzeň's history in a 1–1 home draw against BATE Borisov. On 23 November 2011, he netted the only goal in the away match against Belarusian club BATE Borisov to enable his team to claim its first group stage win and almost assure its progression into the UEFA Europa League as the third best team in the group.